[med-svn] r23957 - in trunk/packages/R/r-bioc-makecdfenv/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Fri Aug 25 19:29:00 UTC 2017
Author: tille
Date: 2017-08-25 19:28:59 +0000 (Fri, 25 Aug 2017)
New Revision: 23957
Added:
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/delete_configure.patch
Modified:
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/changelog
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/compat
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/control
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/series
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
Try hard to build new upstream version but failed
Modified: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/changelog 2017-08-25 12:30:18 UTC (rev 23956)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/changelog 2017-08-25 19:28:59 UTC (rev 23957)
@@ -1,3 +1,12 @@
+r-bioc-makecdfenv (1.52.0-1) unstable; urgency=medium
+
+ * New upstream version
+ * debhelper 10
+ * Standards-Version: 4.1.0 (no changes needed)
+ * Build-Depends: zlib1g-dev
+
+ -- Andreas Tille <tille at debian.org> Fri, 25 Aug 2017 14:27:42 +0200
+
r-bioc-makecdfenv (1.50.0-1) unstable; urgency=medium
* New upstream version
Modified: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/compat 2017-08-25 12:30:18 UTC (rev 23956)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/compat 2017-08-25 19:28:59 UTC (rev 23957)
@@ -1 +1 @@
-9
+10
Modified: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/control 2017-08-25 12:30:18 UTC (rev 23956)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/control 2017-08-25 19:28:59 UTC (rev 23957)
@@ -3,11 +3,12 @@
Uploaders: Andreas Tille <tille at debian.org>
Section: gnu-r
Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 10),
dh-r,
r-base-dev,
- r-bioc-affy (>= 1.44.0)
-Standards-Version: 3.9.8
+ r-bioc-affy (>= 1.44.0),
+ zlib1g-dev
+Standards-Version: 4.1.0
Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-makecdfenv/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-makecdfenv/trunk/
Homepage: https://bioconductor.org/packages/makecdfenv/
Added: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/delete_configure.patch
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/delete_configure.patch (rev 0)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/delete_configure.patch 2017-08-25 19:28:59 UTC (rev 23957)
@@ -0,0 +1,978 @@
+--- a/configure
++++ /dev/null
+@@ -1,975 +0,0 @@
+-#! /bin/sh
+-
+-# Guess values for system-dependent variables and create Makefiles.
+-# Generated automatically using autoconf version 2.13
+-# Copyright (C) 1992, 93, 94, 95, 96 Free Software Foundation, Inc.
+-#
+-# This configure script is free software; the Free Software Foundation
+-# gives unlimited permission to copy, distribute and modify it.
+-
+-# Defaults:
+-ac_help=
+-ac_default_prefix=/usr/local
+-# Any additions from configure.in:
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+-cache_file=./config.cache
+-exec_prefix=NONE
+-host=NONE
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+-sysconfdir='${prefix}/etc'
+-sharedstatedir='${prefix}/com'
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+-includedir='${prefix}/include'
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+-mandir='${prefix}/man'
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+- # Try the directory containing this script, then its parent.
+- ac_prog=$0
+- ac_confdir=`echo $ac_prog|sed 's%/[^/][^/]*$%%'`
+- test "x$ac_confdir" = "x$ac_prog" && ac_confdir=.
+- srcdir=$ac_confdir
+- if test ! -r $srcdir/$ac_unique_file; then
+- srcdir=..
+- fi
+-else
+- ac_srcdir_defaulted=no
+-fi
+-if test ! -r $srcdir/$ac_unique_file; then
+- if test "$ac_srcdir_defaulted" = yes; then
+- { echo "configure: error: can not find sources in $ac_confdir or .." 1>&2; exit 1; }
+- else
+- { echo "configure: error: can not find sources in $srcdir" 1>&2; exit 1; }
+- fi
+-fi
+-srcdir=`echo "${srcdir}" | sed 's%\([^/]\)/*$%\1%'`
+-
+-# Prefer explicitly selected file to automatically selected ones.
+-if test -z "$CONFIG_SITE"; then
+- if test "x$prefix" != xNONE; then
+- CONFIG_SITE="$prefix/share/config.site $prefix/etc/config.site"
+- else
+- CONFIG_SITE="$ac_default_prefix/share/config.site $ac_default_prefix/etc/config.site"
+- fi
+-fi
+-for ac_site_file in $CONFIG_SITE; do
+- if test -r "$ac_site_file"; then
+- echo "loading site script $ac_site_file"
+- . "$ac_site_file"
+- fi
+-done
+-
+-if test -r "$cache_file"; then
+- echo "loading cache $cache_file"
+- . $cache_file
+-else
+- echo "creating cache $cache_file"
+- > $cache_file
+-fi
+-
+-ac_ext=c
+-# CFLAGS is not in ac_cpp because -g, -O, etc. are not valid cpp options.
+-ac_cpp='$CPP $CPPFLAGS'
+-ac_compile='${CC-cc} -c $CFLAGS $CPPFLAGS conftest.$ac_ext 1>&5'
+-ac_link='${CC-cc} -o conftest${ac_exeext} $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS 1>&5'
+-cross_compiling=$ac_cv_prog_cc_cross
+-
+-ac_exeext=
+-ac_objext=o
+-if (echo "testing\c"; echo 1,2,3) | grep c >/dev/null; then
+- # Stardent Vistra SVR4 grep lacks -e, says ghazi at caip.rutgers.edu.
+- if (echo -n testing; echo 1,2,3) | sed s/-n/xn/ | grep xn >/dev/null; then
+- ac_n= ac_c='
+-' ac_t=' '
+- else
+- ac_n=-n ac_c= ac_t=
+- fi
+-else
+- ac_n= ac_c='\c' ac_t=
+-fi
+-
+-
+-
+-
+-
+-
+-echo $ac_n "checking how to run the C preprocessor""... $ac_c" 1>&6
+-echo "configure:530: checking how to run the C preprocessor" >&5
+-# On Suns, sometimes $CPP names a directory.
+-if test -n "$CPP" && test -d "$CPP"; then
+- CPP=
+-fi
+-if test -z "$CPP"; then
+-if eval "test \"`echo '$''{'ac_cv_prog_CPP'+set}'`\" = set"; then
+- echo $ac_n "(cached) $ac_c" 1>&6
+-else
+- # This must be in double quotes, not single quotes, because CPP may get
+- # substituted into the Makefile and "${CC-cc}" will confuse make.
+- CPP="${CC-cc} -E"
+- # On the NeXT, cc -E runs the code through the compiler's parser,
+- # not just through cpp.
+- cat > conftest.$ac_ext <<EOF
+-#line 545 "configure"
+-#include "confdefs.h"
+-#include <assert.h>
+-Syntax Error
+-EOF
+-ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
+-{ (eval echo configure:551: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+-ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
+-if test -z "$ac_err"; then
+- :
+-else
+- echo "$ac_err" >&5
+- echo "configure: failed program was:" >&5
+- cat conftest.$ac_ext >&5
+- rm -rf conftest*
+- CPP="${CC-cc} -E -traditional-cpp"
+- cat > conftest.$ac_ext <<EOF
+-#line 562 "configure"
+-#include "confdefs.h"
+-#include <assert.h>
+-Syntax Error
+-EOF
+-ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
+-{ (eval echo configure:568: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+-ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
+-if test -z "$ac_err"; then
+- :
+-else
+- echo "$ac_err" >&5
+- echo "configure: failed program was:" >&5
+- cat conftest.$ac_ext >&5
+- rm -rf conftest*
+- CPP="${CC-cc} -nologo -E"
+- cat > conftest.$ac_ext <<EOF
+-#line 579 "configure"
+-#include "confdefs.h"
+-#include <assert.h>
+-Syntax Error
+-EOF
+-ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
+-{ (eval echo configure:585: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+-ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
+-if test -z "$ac_err"; then
+- :
+-else
+- echo "$ac_err" >&5
+- echo "configure: failed program was:" >&5
+- cat conftest.$ac_ext >&5
+- rm -rf conftest*
+- CPP=/lib/cpp
+-fi
+-rm -f conftest*
+-fi
+-rm -f conftest*
+-fi
+-rm -f conftest*
+- ac_cv_prog_CPP="$CPP"
+-fi
+- CPP="$ac_cv_prog_CPP"
+-else
+- ac_cv_prog_CPP="$CPP"
+-fi
+-echo "$ac_t""$CPP" 1>&6
+-
+-
+- have_zlib=no
+- echo $ac_n "checking for main in -lz""... $ac_c" 1>&6
+-echo "configure:612: checking for main in -lz" >&5
+-ac_lib_var=`echo z'_'main | sed 'y%./+-%__p_%'`
+-if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
+- echo $ac_n "(cached) $ac_c" 1>&6
+-else
+- ac_save_LIBS="$LIBS"
+-LIBS="-lz $LIBS"
+-cat > conftest.$ac_ext <<EOF
+-#line 620 "configure"
+-#include "confdefs.h"
+-
+-int main() {
+-main()
+-; return 0; }
+-EOF
+-if { (eval echo configure:627: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+- rm -rf conftest*
+- eval "ac_cv_lib_$ac_lib_var=yes"
+-else
+- echo "configure: failed program was:" >&5
+- cat conftest.$ac_ext >&5
+- rm -rf conftest*
+- eval "ac_cv_lib_$ac_lib_var=no"
+-fi
+-rm -f conftest*
+-LIBS="$ac_save_LIBS"
+-
+-fi
+-if eval "test \"`echo '$ac_cv_lib_'$ac_lib_var`\" = yes"; then
+- echo "$ac_t""yes" 1>&6
+-
+- ac_safe=`echo "zlib.h" | sed 'y%./+-%__p_%'`
+-echo $ac_n "checking for zlib.h""... $ac_c" 1>&6
+-echo "configure:645: checking for zlib.h" >&5
+-if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then
+- echo $ac_n "(cached) $ac_c" 1>&6
+-else
+- cat > conftest.$ac_ext <<EOF
+-#line 650 "configure"
+-#include "confdefs.h"
+-#include <zlib.h>
+-EOF
+-ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
+-{ (eval echo configure:655: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+-ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
+-if test -z "$ac_err"; then
+- rm -rf conftest*
+- eval "ac_cv_header_$ac_safe=yes"
+-else
+- echo "$ac_err" >&5
+- echo "configure: failed program was:" >&5
+- cat conftest.$ac_ext >&5
+- rm -rf conftest*
+- eval "ac_cv_header_$ac_safe=no"
+-fi
+-rm -f conftest*
+-fi
+-if eval "test \"`echo '$ac_cv_header_'$ac_safe`\" = yes"; then
+- echo "$ac_t""yes" 1>&6
+-
+- echo $ac_n "checking if zlib version >= 1.1.3""... $ac_c" 1>&6
+-echo "configure:673: checking if zlib version >= 1.1.3" >&5
+- if test "$cross_compiling" = yes; then
+- echo "$ac_t""no" 1>&6
+-else
+- cat > conftest.$ac_ext <<EOF
+-#line 678 "configure"
+-#include "confdefs.h"
+-
+-#include "confdefs.h"
+-#include <string.h>
+-#include <zlib.h>
+-int main() {
+-#ifdef ZLIB_VERSION
+- return(strcmp(ZLIB_VERSION, "1.1.3") < 0);
+-#else
+- return(1);
+-#endif
+-}
+-EOF
+-if { (eval echo configure:692: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext} && (./conftest; exit) 2>/dev/null
+-then
+- echo "$ac_t""yes" 1>&6
+- have_zlib=yes
+-else
+- echo "configure: failed program was:" >&5
+- cat conftest.$ac_ext >&5
+- rm -fr conftest*
+- echo "$ac_t""no" 1>&6
+-fi
+-rm -fr conftest*
+-fi
+-
+-
+-else
+- echo "$ac_t""no" 1>&6
+-fi
+-
+-
+-else
+- echo "$ac_t""no" 1>&6
+-fi
+-
+- if test "${have_zlib}" = yes; then
+- cat >> confdefs.h <<\EOF
+-#define HAVE_ZLIB 1
+-EOF
+-
+- LIBS='-lz '$LIBS
+- fi
+-
+-
+-
+-trap '' 1 2 15
+-cat > confcache <<\EOF
+-# This file is a shell script that caches the results of configure
+-# tests run on this system so they can be shared between configure
+-# scripts and configure runs. It is not useful on other systems.
+-# If it contains results you don't want to keep, you may remove or edit it.
+-#
+-# By default, configure uses ./config.cache as the cache file,
+-# creating it if it does not exist already. You can give configure
+-# the --cache-file=FILE option to use a different cache file; that is
+-# what configure does when it calls configure scripts in
+-# subdirectories, so they share the cache.
+-# Giving --cache-file=/dev/null disables caching, for debugging configure.
+-# config.status only pays attention to the cache file if you give it the
+-# --recheck option to rerun configure.
+-#
+-EOF
+-# The following way of writing the cache mishandles newlines in values,
+-# but we know of no workaround that is simple, portable, and efficient.
+-# So, don't put newlines in cache variables' values.
+-# Ultrix sh set writes to stderr and can't be redirected directly,
+-# and sets the high bit in the cache file unless we assign to the vars.
+-(set) 2>&1 |
+- case `(ac_space=' '; set | grep ac_space) 2>&1` in
+- *ac_space=\ *)
+- # `set' does not quote correctly, so add quotes (double-quote substitution
+- # turns \\\\ into \\, and sed turns \\ into \).
+- sed -n \
+- -e "s/'/'\\\\''/g" \
+- -e "s/^\\([a-zA-Z0-9_]*_cv_[a-zA-Z0-9_]*\\)=\\(.*\\)/\\1=\${\\1='\\2'}/p"
+- ;;
+- *)
+- # `set' quotes correctly as required by POSIX, so do not add quotes.
+- sed -n -e 's/^\([a-zA-Z0-9_]*_cv_[a-zA-Z0-9_]*\)=\(.*\)/\1=${\1=\2}/p'
+- ;;
+- esac >> confcache
+-if cmp -s $cache_file confcache; then
+- :
+-else
+- if test -w $cache_file; then
+- echo "updating cache $cache_file"
+- cat confcache > $cache_file
+- else
+- echo "not updating unwritable cache $cache_file"
+- fi
+-fi
+-rm -f confcache
+-
+-trap 'rm -fr conftest* confdefs* core core.* *.core $ac_clean_files; exit 1' 1 2 15
+-
+-test "x$prefix" = xNONE && prefix=$ac_default_prefix
+-# Let make expand exec_prefix.
+-test "x$exec_prefix" = xNONE && exec_prefix='${prefix}'
+-
+-# Any assignment to VPATH causes Sun make to only execute
+-# the first set of double-colon rules, so remove it if not needed.
+-# If there is a colon in the path, we need to keep it.
+-if test "x$srcdir" = x.; then
+- ac_vpsub='/^[ ]*VPATH[ ]*=[^:]*$/d'
+-fi
+-
+-trap 'rm -f $CONFIG_STATUS conftest*; exit 1' 1 2 15
+-
+-# Transform confdefs.h into DEFS.
+-# Protect against shell expansion while executing Makefile rules.
+-# Protect against Makefile macro expansion.
+-cat > conftest.defs <<\EOF
+-s%#define \([A-Za-z_][A-Za-z0-9_]*\) *\(.*\)%-D\1=\2%g
+-s%[ `~#$^&*(){}\\|;'"<>?]%\\&%g
+-s%\[%\\&%g
+-s%\]%\\&%g
+-s%\$%$$%g
+-EOF
+-DEFS=`sed -f conftest.defs confdefs.h | tr '\012' ' '`
+-rm -f conftest.defs
+-
+-
+-# Without the "./", some shells look in PATH for config.status.
+-: ${CONFIG_STATUS=./config.status}
+-
+-echo creating $CONFIG_STATUS
+-rm -f $CONFIG_STATUS
+-cat > $CONFIG_STATUS <<EOF
+-#! /bin/sh
+-# Generated automatically by configure.
+-# Run this file to recreate the current configuration.
+-# This directory was configured as follows,
+-# on host `(hostname || uname -n) 2>/dev/null | sed 1q`:
+-#
+-# $0 $ac_configure_args
+-#
+-# Compiler output produced by configure, useful for debugging
+-# configure, is in ./config.log if it exists.
+-
+-ac_cs_usage="Usage: $CONFIG_STATUS [--recheck] [--version] [--help]"
+-for ac_option
+-do
+- case "\$ac_option" in
+- -recheck | --recheck | --rechec | --reche | --rech | --rec | --re | --r)
+- echo "running \${CONFIG_SHELL-/bin/sh} $0 $ac_configure_args --no-create --no-recursion"
+- exec \${CONFIG_SHELL-/bin/sh} $0 $ac_configure_args --no-create --no-recursion ;;
+- -version | --version | --versio | --versi | --vers | --ver | --ve | --v)
+- echo "$CONFIG_STATUS generated by autoconf version 2.13"
+- exit 0 ;;
+- -help | --help | --hel | --he | --h)
+- echo "\$ac_cs_usage"; exit 0 ;;
+- *) echo "\$ac_cs_usage"; exit 1 ;;
+- esac
+-done
+-
+-ac_given_srcdir=$srcdir
+-
+-trap 'rm -fr `echo "src/Makevars" | sed "s/:[^ ]*//g"` conftest*; exit 1' 1 2 15
+-EOF
+-cat >> $CONFIG_STATUS <<EOF
+-
+-# Protect against being on the right side of a sed subst in config.status.
+-sed 's/%@/@@/; s/@%/@@/; s/%g\$/@g/; /@g\$/s/[\\\\&%]/\\\\&/g;
+- s/@@/%@/; s/@@/@%/; s/@g\$/%g/' > conftest.subs <<\\CEOF
+-$ac_vpsub
+-$extrasub
+-s%@SHELL@%$SHELL%g
+-s%@CFLAGS@%$CFLAGS%g
+-s%@CPPFLAGS@%$CPPFLAGS%g
+-s%@CXXFLAGS@%$CXXFLAGS%g
+-s%@FFLAGS@%$FFLAGS%g
+-s%@DEFS@%$DEFS%g
+-s%@LDFLAGS@%$LDFLAGS%g
+-s%@LIBS@%$LIBS%g
+-s%@exec_prefix@%$exec_prefix%g
+-s%@prefix@%$prefix%g
+-s%@program_transform_name@%$program_transform_name%g
+-s%@bindir@%$bindir%g
+-s%@sbindir@%$sbindir%g
+-s%@libexecdir@%$libexecdir%g
+-s%@datadir@%$datadir%g
+-s%@sysconfdir@%$sysconfdir%g
+-s%@sharedstatedir@%$sharedstatedir%g
+-s%@localstatedir@%$localstatedir%g
+-s%@libdir@%$libdir%g
+-s%@includedir@%$includedir%g
+-s%@oldincludedir@%$oldincludedir%g
+-s%@infodir@%$infodir%g
+-s%@mandir@%$mandir%g
+-s%@CPP@%$CPP%g
+-
+-CEOF
+-EOF
+-
+-cat >> $CONFIG_STATUS <<\EOF
+-
+-# Split the substitutions into bite-sized pieces for seds with
+-# small command number limits, like on Digital OSF/1 and HP-UX.
+-ac_max_sed_cmds=90 # Maximum number of lines to put in a sed script.
+-ac_file=1 # Number of current file.
+-ac_beg=1 # First line for current file.
+-ac_end=$ac_max_sed_cmds # Line after last line for current file.
+-ac_more_lines=:
+-ac_sed_cmds=""
+-while $ac_more_lines; do
+- if test $ac_beg -gt 1; then
+- sed "1,${ac_beg}d; ${ac_end}q" conftest.subs > conftest.s$ac_file
+- else
+- sed "${ac_end}q" conftest.subs > conftest.s$ac_file
+- fi
+- if test ! -s conftest.s$ac_file; then
+- ac_more_lines=false
+- rm -f conftest.s$ac_file
+- else
+- if test -z "$ac_sed_cmds"; then
+- ac_sed_cmds="sed -f conftest.s$ac_file"
+- else
+- ac_sed_cmds="$ac_sed_cmds | sed -f conftest.s$ac_file"
+- fi
+- ac_file=`expr $ac_file + 1`
+- ac_beg=$ac_end
+- ac_end=`expr $ac_end + $ac_max_sed_cmds`
+- fi
+-done
+-if test -z "$ac_sed_cmds"; then
+- ac_sed_cmds=cat
+-fi
+-EOF
+-
+-cat >> $CONFIG_STATUS <<EOF
+-
+-CONFIG_FILES=\${CONFIG_FILES-"src/Makevars"}
+-EOF
+-cat >> $CONFIG_STATUS <<\EOF
+-for ac_file in .. $CONFIG_FILES; do if test "x$ac_file" != x..; then
+- # Support "outfile[:infile[:infile...]]", defaulting infile="outfile.in".
+- case "$ac_file" in
+- *:*) ac_file_in=`echo "$ac_file"|sed 's%[^:]*:%%'`
+- ac_file=`echo "$ac_file"|sed 's%:.*%%'` ;;
+- *) ac_file_in="${ac_file}.in" ;;
+- esac
+-
+- # Adjust a relative srcdir, top_srcdir, and INSTALL for subdirectories.
+-
+- # Remove last slash and all that follows it. Not all systems have dirname.
+- ac_dir=`echo $ac_file|sed 's%/[^/][^/]*$%%'`
+- if test "$ac_dir" != "$ac_file" && test "$ac_dir" != .; then
+- # The file is in a subdirectory.
+- test ! -d "$ac_dir" && mkdir "$ac_dir"
+- ac_dir_suffix="/`echo $ac_dir|sed 's%^\./%%'`"
+- # A "../" for each directory in $ac_dir_suffix.
+- ac_dots=`echo $ac_dir_suffix|sed 's%/[^/]*%../%g'`
+- else
+- ac_dir_suffix= ac_dots=
+- fi
+-
+- case "$ac_given_srcdir" in
+- .) srcdir=.
+- if test -z "$ac_dots"; then top_srcdir=.
+- else top_srcdir=`echo $ac_dots|sed 's%/$%%'`; fi ;;
+- /*) srcdir="$ac_given_srcdir$ac_dir_suffix"; top_srcdir="$ac_given_srcdir" ;;
+- *) # Relative path.
+- srcdir="$ac_dots$ac_given_srcdir$ac_dir_suffix"
+- top_srcdir="$ac_dots$ac_given_srcdir" ;;
+- esac
+-
+-
+- echo creating "$ac_file"
+- rm -f "$ac_file"
+- configure_input="Generated automatically from `echo $ac_file_in|sed 's%.*/%%'` by configure."
+- case "$ac_file" in
+- *Makefile*) ac_comsub="1i\\
+-# $configure_input" ;;
+- *) ac_comsub= ;;
+- esac
+-
+- ac_file_inputs=`echo $ac_file_in|sed -e "s%^%$ac_given_srcdir/%" -e "s%:% $ac_given_srcdir/%g"`
+- sed -e "$ac_comsub
+-s%@configure_input@%$configure_input%g
+-s%@srcdir@%$srcdir%g
+-s%@top_srcdir@%$top_srcdir%g
+-" $ac_file_inputs | (eval "$ac_sed_cmds") > $ac_file
+-fi; done
+-rm -f conftest.s*
+-
+-EOF
+-cat >> $CONFIG_STATUS <<EOF
+-
+-EOF
+-cat >> $CONFIG_STATUS <<\EOF
+-
+-exit 0
+-EOF
+-chmod +x $CONFIG_STATUS
+-rm -fr confdefs* $ac_clean_files
+-test "$no_create" = yes || ${CONFIG_SHELL-/bin/sh} $CONFIG_STATUS || exit 1
+-
Modified: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/series 2017-08-25 12:30:18 UTC (rev 23956)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/series 2017-08-25 19:28:59 UTC (rev 23957)
@@ -1 +1,2 @@
use_debian_packaged_zlib.patch
+delete_configure.patch
Modified: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/use_debian_packaged_zlib.patch 2017-08-25 12:30:18 UTC (rev 23956)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/patches/use_debian_packaged_zlib.patch 2017-08-25 19:28:59 UTC (rev 23957)
@@ -25,3 +25,13 @@
importFrom(affy, cleancdfname)
importFrom(Biobase, createPackage, multiassign)
+--- a/configure.in
++++ b/configure.in
+@@ -21,7 +21,5 @@ dnl tests the zlib.h
+ dnl (the test is found in 'acinclude.m4')
+ dnl
+
+-R_ZLIB
+-
+
+ AC_OUTPUT(src/Makevars)
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