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dp

Member

From: Zürich, Switzerland

Registered: 2003-05-27

Posts: 3,378

Website

ncbi-toolbox

building with shared libs on:

# $Id: PKGBUILD,v 1.1 2004/09/22 13:21:15 damir Exp $
# Maintainter: Damir Perisa <damir.perisa@bluewin.ch>
pkgname=ncbi-toolbox
provides=('blast' 'sequin' 'fa2htgs' 'entrez' 'cn3d')
pkgver=6.1
pkgrel=1
pkgdesc="The NCBI Software Development Toolkit was developed for the production and distribution of GenBank, Entrez, BLAST, and related services by NCBI."
url="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/README.htm"
source=(ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/CURRENT/ncbi.tar.gz)
depends=('glibc')
makedepends=('tcsh' 'sed')
install=$pkgname.install

entrez_data_dir=/usr/share/entrez/data/

build() {
  cd $startdir/src/
  # csh -> tcsh [we are not unix!]
  sed -i 's|#!/bin/csh -f|#!/usr/bin/tcsh -f|g' 
       $startdir/src/ncbi/make/{makedis.csh,ln-if-absent}

  # messing about makefile (makeall.unx is the makefile)
  sed -i '64s|CC = cc|CC="gcc -ansi"|' 
       $startdir/src/ncbi/make/makeall.unx || return 1
  sed -i '68s|VIBLIBS = |VIBLIBS="-L/usr/X11R6/lib -lXm -lXpm -lXmu -lXp -lXt -lX11 -lXext"|' 
       $startdir/src/ncbi/make/makeall.unx || return 1
  sed -i '155s|NCBI_SHLIBS =||' 
       $startdir/src/ncbi/make/makeall.unx || return 1

  # action!
  $startdir/src/ncbi/make/makedis.csh - 2>&1 | tee out.makedis.csh || return 1

  # install libs:
  mkdir -p $startdir/pkg/usr/lib
  cp -r $startdir/src/ncbi/lib/* $startdir/pkg/usr/lib

  # install bins:
  mkdir -p $startdir/pkg/usr/bin
  cp -r $startdir/src/ncbi/bin/* $startdir/pkg/usr/bin

  # install man pages:
  mkdir -p $startdir/pkg/usr/man/man1
  cp -r $startdir/src/ncbi/doc/man/*.1 $startdir/pkg/usr/man/man1

  # add data to pkg:
  mkdir -p $startdir/pkg${entrez_data_dir}
  cp -r $startdir/src/ncbi/data/* $startdir/pkg${entrez_data_dir}

  echo "[NCBI]" >> $startdir/pkg/etc/ncbi/ncbirc
  echo "Data=${entrez_data_dir}" >> $startdir/pkg/etc/ncbi/ncbirc
}

results in this errors:

gcc -pipe -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -o Psequin -I. -O3 -mcpu=pentiumpro -I../include -L../lib -I/usr/X11R6/include -L/usr/X11R6/lib -DWIN_MOTIF -UINTERNAL_NCBI_SEQUIN sequin1.c sequin2.c sequin3.c sequin4.c sequin5.c sequin6.c sequin7.c sequin8.c sequin9.c sequin10.c sequinx.c 
-lncbicn3d -lddvlib -lblastapi -lblast -lvibnet -lncbidesk -lncbimmdb -lncbitxc2 -lncbiid1 -lnetblast -lncbitool -lncbimla 
-lncbiNacc -lnetentr -lnetcli -lncbicdr -lvibrant -lncbiobj -lncbi -L/usr/X11R6/lib -lXmu -lXm -lXt -lSM -lICE -lXext -lXp -lX11 -ldl -lm
`-mcpu=' is deprecated. Use `-mtune=' or '-march=' instead.
sequin2.c: In function `ImportFastaDialog':
sequin2.c:566: warning: comparison is always true due to limited range of data type
sequin3.c: In function `RemoveTaxonProc':
sequin3.c:5029: warning: cast from pointer to integer of different size
sequin3.c: In function `RemoveTaxonXrefs':
sequin3.c:5060: warning: cast to pointer from integer of different size
sequin3.c: In function `TruncProtsCallback':
sequin3.c:10076: warning: cast to pointer from integer of different size
sequin5.c: In function `OkToOperateOnSource':
sequin5.c:9468: warning: comparison is always false due to limited range of data type
sequin7.c: In function `RemoveAlignmentCallback':
sequin7.c:8261: warning: comparison is always true due to limited range of data type
sequin9.c: In function `ReplaceQualityScores':
sequin9.c:2703: warning: comparison is always false due to limited range of data type
../lib/libncbi.a(ncbifile.o)(.text+0xa3d): In function `Nlm_TmpNam':
: warning: the use of `tempnam' is dangerous, better use `mkstemp'
../lib/libncbitool.a(pobutil.o)(.text+0x406): In function `filter_repeats':
: undefined reference to `DefaultSimPam'
../lib/libncbitool.a(pobutil.o)(.text+0x498): In function `filter_repeats':
: undefined reference to `merge_two_list'

with Arch CURRENT

removing the sed changes that enable shlibs results in successfull build but in _huge_ filesizes (~150mb)

ideas?

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The impossible missions are the only ones which succeed.