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sci-astronomy/esomidas: initial import

Browse Source 
Thanks Cédric Krier for his initial work.
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=148822

Package-Manager: portage-2.2.28
This commit is contained in:
Sébastien Fabbro
2016-04-15 00:17:42 +00:00
parent a851b2296d
commit 187669684e
18 changed files with 792 additions and 0 deletions
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1
sci-astronomy/esomidas/Manifest Normal file
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DIST esomidas-15.09.tar.gz 60770911 SHA256 74f1ea0e4cce958c67f5f2db061a073c9fb05190d9c1f1612e77888282a194be SHA512 774029ac2e79a563a1c94c5de4f7cb74f18695e8f83f3d939208bdde656d1e83783e2ae276ae841a3b5c7eaf81946111c3c02ace1b74899e98f1b1dd15ba320b WHIRLPOOL a7135f9f47fa53dbe60288afbcdf462f3f7327736ae473c43766185b1a57836eb2cf120705d9db495d62a5a26efca533afd6cc5719a7c4c4d224fe301234584e

148
sci-astronomy/esomidas/esomidas-15.09.ebuild Normal file
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# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI=6
inherit eutils fortran-2 toolchain-funcs flag-o-matic
# MIDVERS is actually used by MIDAS configuration scripts
export MIDVERS="15SEPpl1.0"
DESCRIPTION="European Southern Observatory Munich Image Data Analysis System"
HOMEPAGE="http://www.eso.org/projects/esomidas/"
SRC_URI="ftp://ftp.eso.org/pub/midaspub/15SEP/sources/${MIDVERS}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0/8"
KEYWORDS="~amd64 ~x86"
IUSE=""
RDEPEND="
sys-libs/readline:0=
x11-libs/motif:0=
x11-libs/libX11:=
x11-libs/libXt:="
DEPEND="${RDEPEND}"
S="${WORKDIR}/${MIDVERS}"
PATCHES=(
"${FILESDIR}/${PN}-gentoo-setup.patch"
"${FILESDIR}/${PN}-cleanmidas.patch"
"${FILESDIR}/${PN}-fitswdb.patch"
"${FILESDIR}/${PN}-fitswdm_c.patch"
"${FILESDIR}/${PN}-log-stdout.patch"
"${FILESDIR}/${PN}-manpages.patch"
"${FILESDIR}/${PN}-mdb_put.patch"
"${FILESDIR}/${PN}-no-sp_pty.patch"
"${FILESDIR}/${PN}-no-strip.patch"
"${FILESDIR}/${PN}-rarthm_for.patch"
"${FILESDIR}/${PN}-selechar_c.patch"
"${FILESDIR}/${PN}-system-readline.patch"
"${FILESDIR}/${PN}-x11-include-path.patch"
"${FILESDIR}/${PN}-propagate-flags.patch"
"${FILESDIR}/${PN}-syskeys.patch"
)
src_prepare() {
default
# variables for all phases and midas internal build system
export MIDASHOME="${WORKDIR}"
export MID_HOME="${S}"
export MID_HOME0="/usr/$(get_libdir)/esomidas/${MIDVERS}"
export MID_INSTALL="${MID_HOME}/install/unix"
export MID_SYS="${MID_HOME}/system/unix/"
export MID_WORK="${MIDASHOME}/midwork"
# create a gentoo option file
mkdir ${MID_INSTALL}/systems/Gentoo || die
cat >> ${MID_INSTALL}/systems/Gentoo/make_options <<-EOF
CC=$(tc-getCC)
LDCC=$(tc-getCC)
F77=$(tc-getFC)
FC=$(tc-getFC)
LD77_CMD=$(tc-getFC)
AR=$(tc-getAR)
RANLIB=$(tc-getRANLIB)
F_OPT=
C_OPT=
E_OPT=$(use amd64 && echo -Z)
SYS=
SH_OPT=-fPIC
SH_CMD=${MIDASHOME}/${MIDVERS}/local/make_shared
GUI_OPT=-DPATH_MAX=1024
STRIP=echo
EDITFLAGS=-DVOID_SIGHANDLER -DHAVE_ALLOCA -DHAVE_ALLOCA_H -DHAVE_GETPW_DECLS -DHAVE_DIRENT_H -DHAVE_STRING_H -DLinux -DHAVE_UNISTD_H -DHAVE_STDLIB_H
EDITLIBS=-lreadline
UIMX=uimxR5
INSTALL_FLAG=auto
EOF
sed -e "s|gcc|$(tc-getCC) \${LDFLAGS}|" \
${MID_INSTALL}/systems/Linux/make_shared \
> ${MID_INSTALL}/systems/Gentoo/make_shared || die
sed -e 's|PC/Linux|Gentoo|' \
${MID_INSTALL}/systems/Linux/setup \
> ${MID_INSTALL}/systems/Gentoo/setup || die
# gentoo readline avoids exporting the xmalloc,xrealloc and xfree
append-cppflags -Dxrealloc=_rl_realloc -Dxmalloc=_rl_malloc -Dxfree=_rl_free
}
src_configure() {
${MID_INSTALL}/select all || die "packages selection failed"
${MID_INSTALL}/preinstall -a || die "preinstallation failed"
${MID_INSTALL}/install2 || die "configuration failed"
chmod 755 ${MID_HOME}/local/make_shared
}
src_compile() {
CMND_YES=2 ${MID_INSTALL}/install3 -a || die "compilation failed"
[[ -x ${MID_HOME}/monit/midasgo.exe ]] || die "somewhere compilation failed"
emake -C monit syskeys.unix
${MID_SYS}/inmidas -m ${MID_WORK} -j "@ compile.all"
${MID_SYS}/inmidas -m ${MID_WORK} -j "@ ascii_bin no ; bye"
}
src_test() {
local test_dir="${WORKDIR}/test_tmp"
mkdir ${test_dir} && cd ${test_dir}
${MID_SYS}/inmidas -m ${MID_WORK} -j "@ vericopy ; @@ veriall -nodisplay ; bye" || die
test -f ${MID_WORK}/veriall_* || die "tests failed somewhere"
rm -rf ${test_dir}
}
src_install() {
yes | ${MID_SYS}/cleanmidas
find ${MID_HOME} \( \
-name "*.a" -o \
-name "makefile" -o \
-name "default.mk" -o \
-name "*.h" -o \
-name "*.inc" -o \
-name COPYING -o \
-name "*~" -o \
-name "*.mod" \) -delete
rm -rf ${MID_HOME}/libsrc/ftoc*
find ${MID_HOME} -type d -empty -delete
sed -e "s:^MIDVERS0=.*:MIDVERS0=${MIDVERS}:" \
-e "s:^MIDASHOME0=.*:MIDASHOME0=/usr/$(get_libdir)/esomidas:" \
-i ${MID_HOME}/system/unix/{inmidas,helpmidas,drs}
cd "${WORKDIR}"
dodir /usr/$(get_libdir)/esomidas
mv "${S}" "${ED}"${MID_HOME0}
chmod 0644 "${ED}"${MID_HOME0}/contrib/baches/*/*.fit \
"${ED}"${MID_HOME0}/contrib/baches/*/*.fmt \
"${ED}"${MID_HOME0}/contrib/baches/*/*.datorg \
"${ED}"${MID_HOME0}/contrib/baches/*/*.prg \
"${ED}"${MID_HOME0}/contrib/baches/*/*.README
find "${ED}"${MID_HOME0} -name \*.sh | xargs chmod 0755
chmod 0755 "${ED}"${MID_HOME0}/util/bench/brun
dosym ${MID_HOME0}/system/unix/inmidas /usr/bin/inmidas
dosym ${MID_HOME0}/system/unix/gomidas /usr/bin/gomidas
dosym ${MID_HOME0}/system/ftoc-new ${MID_HOME0}/system/good-ftoc
}

24
sci-astronomy/esomidas/files/esomidas-cleanmidas.patch Normal file
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@@ -0,0 +1,24 @@
Author: Ole Streicher <olebole@debian.org>
Description: Use predefined MIDVERS and MIDASHOME in cleanmidas
Cleanmidas assumes the the parent directory of "15FEBpl1.1" is "midas",
which is not required in the installation guide.
--- a/system/unix/cleanmidas
+++ b/system/unix/cleanmidas
@@ -54,11 +54,13 @@
[ $answer = y ]
}
-
MID_HERE=`pwd`
-MIDVERS=`echo $MID_HERE | sed 's/^.*midas\/\([^\/]*\).*$/\1/'`
-MIDASHOME=`echo $MID_HERE | sed 's/\/'$MIDVERS'.*$//'`
-
+if [ -z "$MIDVERS" ] ; then
+ MIDVERS=`echo $MID_HERE | sed 's/^.*midas\/\([^\/]*\).*$/\1/'`
+fi
+if [ -z "$MIDASHOME" ] ; then
+ MIDASHOME=`echo $MID_HERE | sed 's/\/'$MIDVERS'.*$//'`
+fi
MID_HOME=$MIDASHOME/$MIDVERS
export MIDASHOME MIDVERS

46
sci-astronomy/esomidas/files/esomidas-fitswdb.patch Normal file
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@@ -0,0 +1,46 @@
Author: Ole Streicher <olebole@debian.org>
Description: Another off-by-one
Fixes:
.
ERROR: AddressSanitizer: stack-buffer-overflow on address 0x7fff9e7713b1 at pc 0x7f4135c48c7c bp 0x7fff9e770e20 sp 0x7fff9e770e18
WRITE of size 1 at 0x7fff9e7713b1 thread T0
#0 0x7f4135c48c7b in fitswdb prim/dio/libsrc/fitswdb.c:243
#1 0x7f4135c4a61c in fitswhd prim/dio/libsrc/fitswhd.c:450
#2 0x7f4135caab6e in SCFSAV libsrc/st/scfa.c:157
#3 0x7f4135caff75 in SCFCLO libsrc/st/scfb.c:483
#4 0x7f4135cba83e in SCSEPI libsrc/st/scs.c:353
#5 0x7f4135cc6cd8 in stsepi_ libsrc/ftoc/sts.c:67
#6 0x409fb7 in statis prim/display/src/statis.f:1034
#7 0x40549c in main prim/display/src/statis.f:1056
#8 0x7f4134de2b44 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x21b44)
#9 0x405a92 (prim/exec/statis.exe+0x405a92)
Address 0x7fff9e7713b1 is located in stack of thread T0 at offset 1265 in frame
#0 0x7f4135c45c7f in fitswdb prim/dio/libsrc/fitswdb.c:88
This frame has 21 object(s):
[32, 36) 'nv'
[...]
[1056, 1137) 'com'
[1184, 1265) 'cval' <== Memory access at offset 1265 overflows this variable
[1312, 1393) 'line'
[1440, 1521) 'help'
--- a/prim/dio/libsrc/fitswdb.c
+++ b/prim/dio/libsrc/fitswdb.c
@@ -240,12 +240,12 @@
if (dtk->ctl==NCTL || dtk->ctl==SCTL) {
nc = (MXLB<nbp) ? MXLB : nbp;
SCDRDC(mfd,md->name,1,ns,nc,&nv,cval,unit,&null);
- cval[nv] = '\0';
- for (nn=0; nn<nv; nn++)
+ cval[nv-1] = '\0';
+ for (nn=0; nn<nv-1; nn++)
if (cval[nn]<' ' || '~'<cval[nn])
cval[nn] = ' ';
if(dtk->ctl==SCTL) {
- ival = nv-1;
+ ival = nv-2;
while (ival && cval[ival]==' ') ival--;
cval[++ival] = '\0';
}

48
sci-astronomy/esomidas/files/esomidas-fitswdm_c.patch Normal file
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@@ -0,0 +1,48 @@
Author: Ole Streicher <olebole@debian.org>
Description: fix nullification of fitswdm.c
Fitswdm.c uses toNULLLONG to set an integer to some minimal value
(funnily, not 0 but LONG_MIN!). However, this will lead to a wrong
result if long!=int, since the argument is an int. On LinuxAMD64, this
was fixed, but not generally. This patch make the special case for
LinuxAMD64 as the general one.
--- a/prim/dio/libsrc/fitswdm.c
+++ b/prim/dio/libsrc/fitswdm.c
@@ -237,12 +237,7 @@
{ /* NULL fill if needed */
pi = p.i + ns;
i = n - ns;
-
-#ifdef LinuxAMD64
while (i--) toNULLINT (*pi++);
-#else
- while (i--) toNULLLONG (*pi++);
-#endif
}
ioff += n;
np = 4 * ns;
@@ -279,12 +274,7 @@
while (n--)
if (isNULLFLOAT (*pf))
{
-
-#ifdef LinuxAMD64
toNULLINT (*pi++);
-#else
- toNULLLONG (*pi++);
-#endif
*pf++;
}
else
@@ -332,12 +322,7 @@
while (n--)
if (isNULLFLOAT (*pd))
{
-
-#ifdef LinuxAMD64
toNULLINT (*pi++);
-#else
- toNULLLONG (*pi++);
-#endif
*pd++;
}
else

14
sci-astronomy/esomidas/files/esomidas-gentoo-setup.patch Normal file
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@@ -0,0 +1,14 @@
--- a/install/unix/preinstall
+++ b/install/unix/preinstall
@@ -121,7 +121,10 @@
urels=`(uname -r) 2>/dev/null`
machine=`(uname -m) 2>/dev/null`
-if [ "$uname" = "Darwin" ]; then
+if [ -d "Gentoo" -a -f "/etc/gentoo-release" ]; then
+ system="Gentoo"
+
+elif [ "$uname" = "Darwin" ]; then
system="Darwin"
elif [ "$machine" = "x86_64" ]; then

67
sci-astronomy/esomidas/files/esomidas-log-stdout.patch Normal file
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@@ -0,0 +1,67 @@
Author: Ole Streicher <debian@liska.ath.cx>
Description: Run compilation in foreground and write log to stdout
instead of a file.
--- a/install/unix/install3
+++ b/install/unix/install3
@@ -112,8 +112,6 @@
echo ""
echo "WARNING: MIDAS installation will delete all dependent files."
-echo " It will run in background and the output will be sent to"
-echo " the file <$MID_HOME/tmp/install.$$>"
echo ""
echo "Do you want to continue [yn]? (y): " $SV_NONL
unset answ
@@ -138,17 +136,9 @@
# do we have the 'time' command?
if [ $CMND_YES = 2 ] ; then
- /bin/bash $MID_INSTALL/install -i > $MID_HOME/tmp/install.$$ 2>&1 &
+ /bin/bash $MID_INSTALL/install -i
else
- time /bin/bash $MID_INSTALL/install -i > $MID_HOME/tmp/install.$$ 2>&1 &
+ time /bin/bash $MID_INSTALL/install -i
fi
-echo "Running install in background"
-echo "Results are coming in $MID_HOME/tmp/install.$$"
-if [ "$1" = "-a" ]; then
- echo "Waiting for MIDAS installation to finish..." $SV_NONL
- wait
- echo "Finished."
- echo ""
-fi
exit 0
--- a/lib/makefile
+++ b/lib/makefile
@@ -18,7 +18,7 @@
include ../local/default.mk
-DEV_NULL = >/dev/null 2>&1
+DEV_NULL =
LIBMIDAS = $(LIBDIR)/libmidas.a
LIBGMIDAS = $(LIBDIR)/libgmidas.a
--- a/system/ftoc/makefile
+++ b/system/ftoc/makefile
@@ -12,7 +12,7 @@
include ../../local/default.mk
DEV_NULL= >/dev/null 2>&1
-# DEV_NULL=
+DEV_NULL=
M = ../exec
--- a/system/machine/makefile
+++ b/system/machine/makefile
@@ -16,7 +16,7 @@
include ../../local/default.mk
-DEV_NULL= >/dev/null 2>&1
+DEV_NULL=
M = ../exec

54
sci-astronomy/esomidas/files/esomidas-manpages.patch Normal file
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@@ -0,0 +1,54 @@
Author: Ole Streicher <debian@liska.ath.cx>
Description: Put the manpages in chapter "1" instead of "1L".
They are not local in Debian.
--- a/system/unix/man1/gomidas.1
+++ b/system/unix/man1/gomidas.1
@@ -2,7 +2,7 @@
.\" Copyright (c) 1989 European Southern Observatory.
.\" All rights reserved.
.\"
-.TH gomidas 1L "07 July 1993" MIDAS
+.TH gomidas 1 "07 July 1993" MIDAS
.SH NAME
gomidas \- Resume a MIDAS session.
.SH SYNOPSIS
@@ -56,4 +56,4 @@
.IP "\fBMID_WORK\fp"
Startup directory for MIDAS containing previous MIDAS saved-session files.
.SH SEE ALSO
-.IR inmidas(1L)
+.IR inmidas(1)
--- a/system/unix/man1/helpmidas.1
+++ b/system/unix/man1/helpmidas.1
@@ -2,7 +2,7 @@
.\" Copyright (c) 1989 European Southern Observatory.
.\" All rights reserved.
.\"
-.TH helpmidas 1L "07 July 1993" MIDAS
+.TH helpmidas 1 "07 July 1993" MIDAS
.SH NAME
helpmidas \- Standalone GUI help for MIDAS.
.SH SYNOPSIS
@@ -71,4 +71,4 @@
.IP "\fBMID_WORK\fp"
Startup directory for MIDAS.
.SH SEE ALSO
-.IR inmidas(1L),gomidas(1L)
+.IR inmidas(1),gomidas(1)
--- a/system/unix/man1/inmidas.1
+++ b/system/unix/man1/inmidas.1
@@ -2,7 +2,7 @@
.\" Copyright (c) 1989 European Southern Observatory.
.\" All rights reserved.
.\"
-.TH inmidas 1L "11 November 1994" MIDAS
+.TH inmidas 1 "11 November 1994" MIDAS
.SH NAME
inmidas \- MIDAS start-up procedure for users.
.SH SYNOPSIS
@@ -145,4 +145,4 @@
.IP "\fBMID_WORK\fp"
Startup directory for MIDAS.
.SH SEE ALSO
-.IR gomidas(1L)
+.IR gomidas(1)

29
sci-astronomy/esomidas/files/esomidas-mdb_put.patch Normal file
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@@ -0,0 +1,29 @@
Author: Ole Streicher <olebole@debian.org>
Description: Fix another probably off-by-one error in prim/dio/libsrc/fitsmdb.c
This shall fix the following crash:
.
ERROR: AddressSanitizer: global-buffer-overflow on address 0x7f5ae9867e28 at pc 0x7f5ae979569c bp 0x7fff8c3c744
READ of size 1 at 0x7f5ae9867e28 thread T0
#0 0x7f5ae979569b in mdb_put prim/dio/libsrc/fitsmdb.c:173
#1 0x7f5ae978f489 in fitsckw prim/dio/libsrc/fitsckw.c:872
#2 0x7f5ae97a3ee4 in fitsrhd prim/dio/libsrc/fitsrhd.c:258
#3 0x401ee4 in main prim/dio/src/infile.c:263
#4 0x7f5ae90bab44 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x21b44)
#5 0x4024e2 (prim/exec/infile.exe+0x4024e2)
0x7f5ae9867e28 is located 0 bytes to the right of global variable '*.LC46' from 'fitsckw.c' (0x7f5ae9867e20) of size 8
'*.LC46' is ascii string 'COMMENT'
0x7f5ae9867e28 is located 56 bytes to the left of global variable '*.LC47' from 'fitsckw.c' (0x7f5ae9867e60) of size 3
'*.LC47' is ascii string 'O_'
--- a/prim/dio/libsrc/fitsmdb.c
+++ b/prim/dio/libsrc/fitsmdb.c
@@ -170,7 +170,7 @@
ps = myptr->desc;
pc = kwd->desc;
-for (i=0; i<MXMDN; i++) *ps++ = *pc++;
+strncpy(ps, pc, MXMDN);
myptr->type = kwd->type;
myptr->idx = kwd->idx;

17
sci-astronomy/esomidas/files/esomidas-no-sp_pty.patch Normal file
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@@ -0,0 +1,17 @@
Author: Ole Streicher <olebole@debian.org>
Description: Dont compile gui/GraphLib/libsrc/uimxR5/src/sp_pty.c
This file uses either nonportable termio, or sgtty which is not available
everywhere (again, Hurd and FreeBSD are the examples here). In principle
it could be rewritten to use termios (which is standard today); however
the functions from this file are not needed in midas; therefore it is
simpler just not to compile this.
--- a/gui/GraphLib/libsrc/uimxR5/src/makefile
+++ b/gui/GraphLib/libsrc/uimxR5/src/makefile
@@ -65,7 +65,6 @@
subproc.o\
sp_utils.o\
sp_spmd.o\
- sp_pty.o\
swidget.o \
t_error.o\
uimx.o\

29
sci-astronomy/esomidas/files/esomidas-no-strip.patch Normal file
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@@ -0,0 +1,29 @@
Author: Ole Streicher <olebole@debian.org>
Description: Don't strip binaries during build
This allows a debugging during packaging. The binaries are stripped
later with dh_strip.
--- a/install/unix/install1
+++ b/install/unix/install1
@@ -536,9 +536,9 @@
fi
else
echo "NOT FOUND."
- echo "*** STRIP set to echo."
- ed_moptions add STRIP=echo >/dev/null
fi
+echo "*** STRIP set to echo."
+ed_moptions add STRIP=echo >/dev/null
#*************** END: Checking the strip command **************
#*************** START: Checking the ranlib command ***********
--- a/install/unix/default_mk
+++ b/install/unix/default_mk
@@ -32,7 +32,7 @@
LD77_OPT = $(LDFLAGS)
LD77 = $(LD77_CMD) $(LD77_OPT)
RANLIB = ranlib
-STRIP = strip
+STRIP = echo
AR = ar
AR_OPT = ruv
AR_XOPT = xv

86
sci-astronomy/esomidas/files/esomidas-propagate-flags.patch Normal file
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@@ -0,0 +1,86 @@
Author: Ole Streicher <olebole@debian.org>
Description: Propagate CFLAGS, CPPFLAGS, and FFLAGS
This is done to enable hardening of the code. Also, use -fPIC only
for shared library code.
--- a/install/unix/install1
+++ b/install/unix/install1
@@ -303,7 +303,7 @@
ed_moptions delete C_OPT >/dev/null
ed_moptions delete INSTALL_FLAG >/dev/null
-ed_moptions add "C_OPT=-O $X_OPT" >/dev/null
+ed_moptions add "C_OPT=$X_OPT" >/dev/null
ed_moptions add "K_OPT= $X_OPT" >/dev/null
ed_moptions add "INSTALL_FLAG=auto" >/dev/null
@@ -331,12 +331,13 @@
# 64 bit compiler
else
echo installing Midas on a 64 bit system
- MACH="-m64"
+ MACH=" "
EO="-Z"
fi
ed_moptions add "F77=gfortran $MACH" >/dev/null
-ed_moptions add "LD77_CMD=gfortran $MACH" >/dev/null
+ed_moptions add "LD77_CMD=gfortran $MACH $LDFLAGS" >/dev/null
+ed_moptions add "LDCC=gcc $LDFLAGS" >/dev/null
ed_moptions add "E_OPT= $EO" >/dev/null
--- a/install/unix/default_mk
+++ b/install/unix/default_mk
@@ -49,10 +49,10 @@
E_OPT =
SYS =
SH_CMD = echo
-SH_OPT =
+SH_OPT = -fPIC
SH_EXT = so.8.1
CFLAGS += $(C_OPT) $(DEBUG) $(SYS) $(VARARGS) -I$(INC)
-FFLAGS = $(F_OPT) $(DEBUG) -c
+FFLAGS += $(F_OPT) $(DEBUG) -c
EFLAGS = $(E_OPT) -I$(INC) -I$(LINC) -f
EXFLAGS = -f
SLIB =
--- a/libsrc/ftoc-new/makefile
+++ b/libsrc/ftoc-new/makefile
@@ -21,6 +21,7 @@
C_OPT = $(K_OPT)
CFLAGS += $(C_OPT) $(DEBUG) $(SH_OPT) $(SYS) -I$(INC)
+FFLAGS += $(SH_OPT)
LIB = $(LIBDIR)/libftoc.a
--- a/libsrc/tbl/makefile
+++ b/libsrc/tbl/makefile
@@ -22,6 +22,7 @@
include ../../local/default.mk
CFLAGS += $(C_OPT) $(SH_OPT) $(DEBUG) $(SYS) -I$(INC)
+FFLAGS += $(SH_OPT)
HEADT = $(INC)/tblsys.h $(INC)/tbldef.h $(INC)/tblerr.h
--- a/libsrc/agl/makefile
+++ b/libsrc/agl/makefile
@@ -28,6 +28,7 @@
include ../../local/default.mk
CFLAGS += $(C_OPT) $(DEBUG) $(SH_OPT) $(OSSYS) $(SYS) -I$(INC) $(X11INC) -DMIDAS
+FFLAGS += $(SH_OPT)
LIB = $(LIBDIR)/libagl3.a
M = ../../system/exec
--- a/libsrc/plot/makefile
+++ b/libsrc/plot/makefile
@@ -15,6 +15,7 @@
include ../../local/default.mk
CFLAGS += $(C_OPT) $(SH_OPT) $(DEBUG) $(SYS) -I$(INC)
+FFLAGS += $(SH_OPT)
LIB = $(LIBDIR)/libplot.a

43
sci-astronomy/esomidas/files/esomidas-rarthm_for.patch Normal file
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@@ -0,0 +1,43 @@
Author: Ole Streicher <olebole@debian.org>
Description: Wild-quess workaround for access violations in prim/general/libsrc/calc.for
This is to hide the following problem:
.
ERROR: AddressSanitizer: stack-buffer-overflow on address 0x7fffe7377ec4 at pc 0x40fb5c bp 0x7fffe7377350 sp 0x7fffe7377348
READ of size 4 at 0x7fffe7377ec4 thread T0
#0 0x40fb5b in opffw_ prim/general/libsrc/calc.f:129
#1 0x40900b in rarthm prim/general/src/rarthm.f:402
#2 0x4038ec in main prim/general/src/rarthm.f:456
#3 0x7fed23b91b44 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x21b44)
#4 0x403c42 (prim/exec/rarthm.exe+0x403c42)
Address 0x7fffe7377ec4 is located in stack of thread T0 at offset 1316 in frame
#0 0x40512f in rarthm prim/general/src/rarthm.f:1
This frame has 57 object(s):
[32, 36) 'uni'
[...]
[1184, 1188) 'rownoa'
[1248, 1252) 'rownob'
[1312, 1316) 'rowsiz' <== Memory access at offset 1316 overflows this variable
[1376, 1380) 'stat'
[1440, 1448) 'consta'
[1504, 1512) 'npixa'
[1568, 1576) 'npixb'
[1632, 1640) 'npixc'
--- a/prim/general/src/rarthm.for
+++ b/prim/general/src/rarthm.for
@@ -483,11 +483,11 @@
IF (OPERAT(1:1).NE.'Q') THEN
CALL OPFFW(OPERAT,MADRID(APNTR),MADRID(BPNTR),
+ MADRID(PNTRW),APIX,BPIX,CPIX,
- + ROWSIZ,ROWSIZ,ROWSIZ)
+ + NPIXA,NPIXB,NPIXC)
ELSE
CALL FN2FFW(OPERA(1:5),MADRID(APNTR),MADRID(BPNTR),
+ MADRID(PNTRW),APIX,BPIX,CPIX,
- + ROWSIZ,ROWSIZ,ROWSIZ)
+ + NPIXA,NPIXB,NPIXC)
ENDIF
C
C put resulting row back into relevant ATOM

51
sci-astronomy/esomidas/files/esomidas-selechar_c.patch Normal file
View File

@@ -0,0 +1,51 @@
Author: Ole Streicher <olebole@debian.org>
Description: Fix off-by-one initialization in prim/table/libsrc/selechar.c
I am, however, not sure whether it is in charfun() in selechar.c or SCFMAP()
in scfb.c.
.
It fixes the following crash:
.
ERROR: AddressSanitizer: heap-buffer-overflow on address 0x61a00001f76c at pc 0x42ac5b bp 0x7fffb7a62330 sp 0x7fffb7a62328
WRITE of size 1 at 0x61a00001f76c thread T0
#0 0x42ac5a in charfun prim/table/libsrc/selechar.c:279
#1 0x4154f5 in level5 prim/table/libsrc/tbcomsel.c:797
#2 0x41572a in level4 prim/table/libsrc/tbcomsel.c:720
#3 0x415c57 in level3 prim/table/libsrc/tbcomsel.c:765
#4 0x415d1d in level2 prim/table/libsrc/tbcomsel.c:677
#5 0x41610e in level1 prim/table/libsrc/tbcomsel.c:636
#6 0x4165b0 in level0 prim/table/libsrc/tbcomsel.c:595
#7 0x41415d in level00 prim/table/libsrc/tbcomsel.c:555
#8 0x4179ff in tbl_comp prim/table/libsrc/tbcomsel.c:204
#9 0x4053fd in tk_cexec prim/edit/libsrc/tkeys.c:204
#10 0x404979 in main prim/table/src/tdatatbl.c:107
#11 0x7f1e97ae3b44 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x21b44)
#12 0x404d62 (prim/exec/tdatatbl.exe+0x404d62)
.
0x61a00001f76c is located 0 bytes to the right of 1260-byte region [0x61a00001f280,0x61a00001f76c)
allocated by thread T0 here:
#0 0x7f1e9858373f in malloc (/usr/lib/x86_64-linux-gnu/libasan.so.1+0x5473f)
#1 0x7f1e98241cf2 in SCFMAP libsrc/st/scfb.c:816
#2 0x42a0a3 in charfun prim/table/libsrc/selechar.c:250
#3 0x4154f5 in level5 prim/table/libsrc/tbcomsel.c:797
#4 0x41572a in level4 prim/table/libsrc/tbcomsel.c:720
#5 0x415c57 in level3 prim/table/libsrc/tbcomsel.c:765
#6 0x415d1d in level2 prim/table/libsrc/tbcomsel.c:677
#7 0x41610e in level1 prim/table/libsrc/tbcomsel.c:636
#8 0x4165b0 in level0 prim/table/libsrc/tbcomsel.c:595
#9 0x41415d in level00 prim/table/libsrc/tbcomsel.c:555
#10 0x4179ff in tbl_comp prim/table/libsrc/tbcomsel.c:204
#11 0x4053fd in tk_cexec prim/edit/libsrc/tkeys.c:204
#12 0x404979 in main prim/table/src/tdatatbl.c:107
#13 0x7f1e97ae3b44 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x21b44)
--- a/prim/table/libsrc/selechar.c
+++ b/prim/table/libsrc/selechar.c
@@ -247,7 +247,7 @@
nconst[ibuf[6]] = nchar;
items = nchar * ibuf[2];
SCFCRE(name,D_I1_FORMAT,F_X_MODE,F_IMA_TYPE,items,&imnoc[ibuf[6]]);
- SCFMAP(imnoc[ibuf[6]],F_X_MODE,1,items,&act,&cdata[ibuf[6]]);
+ SCFMAP(imnoc[ibuf[6]],F_X_MODE,1,items+1,&act,&cdata[ibuf[6]]);
}
if (nochar == 0) {
for (i=0, k=0; i<items; i+=nchar,k++) {

23
sci-astronomy/esomidas/files/esomidas-syskeys.patch Normal file
View File

@@ -0,0 +1,23 @@
Author: Ole Streicher <debian@liska.ath.cx>
Description: Write correct syskeys instead of patching in install/unix/setup
--- a/monit/syskeys.datorg
+++ b/monit/syskeys.datorg
@@ -60,7 +60,8 @@
C (31:32) no. of bits for memory addresses (32 or 64)
C SECT./END_OF_KEY
MID$SYS/C/32/R
-Vax/VMS $EDIT 32
+PC/Linux $vi
+C Vax/VMS $EDIT 32
C Sun/Solaris $vi 32
C HP/UX $vi 32
C PC/Linux $vi 32
@@ -426,7 +427,7 @@
C $debugger debug_flags MID$EXE:module options
C SECT./END_OF_KEY
MID$DEBUG/C*40/3/R
-$dbx
+$gdb
?
?
C

83
sci-astronomy/esomidas/files/esomidas-system-readline.patch Normal file
View File

@@ -0,0 +1,83 @@
Author: Ole Streicher <debian@liska.ath.cx>
Description: Use the system provided readline instead of the copy
provided with the sources.
--- a/install/unix/install1
+++ b/install/unix/install1
@@ -576,7 +576,7 @@
then
echo "OK."
ed_moptions replace "EDITSWITCH=-DEdit_dummy" >/dev/null
- ed_moptions replace "EDITLIBS=-lzreadline -lncurses" >/dev/null
+ ed_moptions replace "EDITLIBS=-lreadline" >/dev/null
else
echo "Not found."
echo "*** WARNING: You'll not be able to edit Midas commands in the monitor."
@@ -596,7 +596,7 @@
if [ $answ = "c" -o $answ = "C" ]; then
ed_moptions replace "EDITSWITCH=-DNO_READLINE" >/dev/null
- ed_moptions replace "EDITLIBS=-lzreadline" >/dev/null
+ ed_moptions replace "EDITLIBS=-lreadline" >/dev/null
else
exit 1
fi
--- a/install/unix/install1.sh
+++ b/install/unix/install1.sh
@@ -575,7 +575,7 @@
then
echo "OK."
ed_moptions replace "EDITSWITCH=-DEdit_dummy" >/dev/null
- ed_moptions replace "EDITLIBS=-lzreadline -lncurses" >/dev/null
+ ed_moptions replace "EDITLIBS=-lreadline -lncurses" >/dev/null
else
echo "Not found."
echo "*** WARNING: You'll not be able to edit Midas commands in the monitor."
@@ -595,7 +595,7 @@
if [ $answ = "c" -o $answ = "C" ]; then
ed_moptions replace "EDITSWITCH=-DNO_READLINE" >/dev/null
- ed_moptions replace "EDITLIBS=-lzreadline" >/dev/null
+ ed_moptions replace "EDITLIBS=-lreadline" >/dev/null
else
exit 1
fi
--- a/monit/prepa2.c
+++ b/monit/prepa2.c
@@ -90,6 +90,9 @@
#include <osxdef.h> /* MIDAS osx definitions */
#include <midback.h> /* Context extructure */
+typedef int Function ();
+typedef char **CPPFunction ();
+
extern int is_a_tty; /* Is this a terminal, (yes=1) set in prepa.c */
void using_history();
@@ -238,7 +241,7 @@
if (!xhelp_pid) {
if ( (fd = fopen(channame[1],"r")) == (FILE *)NULL) {
(void) printf("\n\rTry first: CREATE/GUI HELP \n\r");
- rl_refresh_line();
+ rl_refresh_line(0,0);
return 0;
}
fscanf(fd,(const char *) "%d\n",&xhelp_pid);
@@ -247,7 +250,7 @@
xhelp_pid = 0;
unlink(channame[1]);
(void) printf("\n\rTry first: CREATE/GUI HELP \n\r");
- rl_refresh_line();
+ rl_refresh_line(0,0);
return 0;
}
}
--- a/install/unix/core.cnf
+++ b/install/unix/core.cnf
@@ -15,7 +15,6 @@
./libsrc/st
./libsrc/tbl
# ./libsrc/tw FO's termwin library not used anymore...
-./libsrc/readline
./libsrc/agl
./libsrc/plot
./libsrc/display

13
sci-astronomy/esomidas/files/esomidas-x11-include-path.patch Normal file
View File

@@ -0,0 +1,13 @@
Author: Ole Streicher <olebole@debian.org>
Description: Add /usr/include/X11 to the X11 include paths
--- a/install/unix/install1
+++ b/install/unix/install1
@@ -615,7 +615,7 @@
x11incl="found"
else
ed_moptions delete X11INC >/dev/null
- x11inclpth='/usr/openwin/include /usr/include/X11R6 /usr/include/X11R5 /usr/X11R6/include /usr/X11R6/include/X11 /usr/X11R5/include /usr/local/include /include /usr/X/include /opt/X-local/include'
+ x11inclpth='/usr/include/X11 /usr/include/X11R6 /usr/include/X11R5 /usr/X11R6/include /usr/X11R6/include/X11 /usr/X11R5/include /usr/local/include /include /usr/X/include /opt/X-local/include'
for dir in $x11inclpth
do
if [ ! -d $dir ]; then

16
sci-astronomy/esomidas/metadata.xml Normal file
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@@ -0,0 +1,16 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-astronomy@gentoo.org</email>
<name>Gentoo Astronomy Project</name>
</maintainer>
<longdescription lang="en">
The ESO-MIDAS system provides general tools for image processing and data
reduction with emphasis on astronomical applications including imaging and
special reduction packages for ESO instrumentation at La Silla and the VLT at
Paranal. In addition it contains applications packages for stellar and
surface photometry, image sharpening and decomposition, statistics and
various others.
</longdescription>
</pkgmetadata>