commit: 187669684e09edb558fc65bffcb59e9dd2420b0b Author: Sébastien Fabbro <bicatali <AT> gentoo <DOT> org> AuthorDate: Fri Apr 15 00:17:42 2016 +0000 Commit: Sebastien Fabbro <bicatali <AT> gentoo <DOT> org> CommitDate: Fri Apr 15 00:18:16 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=18766968
sci-astronomy/esomidas: initial import Thanks Cédric Krier for his initial work. Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=148822 Package-Manager: portage-2.2.28 sci-astronomy/esomidas/Manifest | 1 + sci-astronomy/esomidas/esomidas-15.09.ebuild | 148 +++++++++++++++++++++ .../esomidas/files/esomidas-cleanmidas.patch | 24 ++++ .../esomidas/files/esomidas-fitswdb.patch | 46 +++++++ .../esomidas/files/esomidas-fitswdm_c.patch | 48 +++++++ .../esomidas/files/esomidas-gentoo-setup.patch | 14 ++ .../esomidas/files/esomidas-log-stdout.patch | 67 ++++++++++ .../esomidas/files/esomidas-manpages.patch | 54 ++++++++ .../esomidas/files/esomidas-mdb_put.patch | 29 ++++ .../esomidas/files/esomidas-no-sp_pty.patch | 17 +++ .../esomidas/files/esomidas-no-strip.patch | 29 ++++ .../esomidas/files/esomidas-propagate-flags.patch | 86 ++++++++++++ .../esomidas/files/esomidas-rarthm_for.patch | 43 ++++++ .../esomidas/files/esomidas-selechar_c.patch | 51 +++++++ .../esomidas/files/esomidas-syskeys.patch | 23 ++++ .../esomidas/files/esomidas-system-readline.patch | 83 ++++++++++++ .../esomidas/files/esomidas-x11-include-path.patch | 13 ++ sci-astronomy/esomidas/metadata.xml | 16 +++ 18 files changed, 792 insertions(+) diff --git a/sci-astronomy/esomidas/Manifest b/sci-astronomy/esomidas/Manifest new file mode 100644 index 0000000..6d71d14 --- /dev/null +++ b/sci-astronomy/esomidas/Manifest @@ -0,0 +1 @@ +DIST esomidas-15.09.tar.gz 60770911 SHA256 74f1ea0e4cce958c67f5f2db061a073c9fb05190d9c1f1612e77888282a194be SHA512 774029ac2e79a563a1c94c5de4f7cb74f18695e8f83f3d939208bdde656d1e83783e2ae276ae841a3b5c7eaf81946111c3c02ace1b74899e98f1b1dd15ba320b WHIRLPOOL a7135f9f47fa53dbe60288afbcdf462f3f7327736ae473c43766185b1a57836eb2cf120705d9db495d62a5a26efca533afd6cc5719a7c4c4d224fe301234584e diff --git a/sci-astronomy/esomidas/esomidas-15.09.ebuild b/sci-astronomy/esomidas/esomidas-15.09.ebuild new file mode 100644 index 0000000..7efe5eb --- /dev/null +++ b/sci-astronomy/esomidas/esomidas-15.09.ebuild @@ -0,0 +1,148 @@ +# 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 +} diff --git a/sci-astronomy/esomidas/files/esomidas-cleanmidas.patch b/sci-astronomy/esomidas/files/esomidas-cleanmidas.patch new file mode 100644 index 0000000..53f2347 --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-cleanmidas.patch @@ -0,0 +1,24 @@ +Author: Ole Streicher <[email protected]> +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 diff --git a/sci-astronomy/esomidas/files/esomidas-fitswdb.patch b/sci-astronomy/esomidas/files/esomidas-fitswdb.patch new file mode 100644 index 0000000..b0459a1 --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-fitswdb.patch @@ -0,0 +1,46 @@ +Author: Ole Streicher <[email protected]> +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'; + } diff --git a/sci-astronomy/esomidas/files/esomidas-fitswdm_c.patch b/sci-astronomy/esomidas/files/esomidas-fitswdm_c.patch new file mode 100644 index 0000000..625208d --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-fitswdm_c.patch @@ -0,0 +1,48 @@ +Author: Ole Streicher <[email protected]> +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 diff --git a/sci-astronomy/esomidas/files/esomidas-gentoo-setup.patch b/sci-astronomy/esomidas/files/esomidas-gentoo-setup.patch new file mode 100644 index 0000000..8b894bb --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-gentoo-setup.patch @@ -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 diff --git a/sci-astronomy/esomidas/files/esomidas-log-stdout.patch b/sci-astronomy/esomidas/files/esomidas-log-stdout.patch new file mode 100644 index 0000000..b7cc376 --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-log-stdout.patch @@ -0,0 +1,67 @@ +Author: Ole Streicher <[email protected]> +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 + diff --git a/sci-astronomy/esomidas/files/esomidas-manpages.patch b/sci-astronomy/esomidas/files/esomidas-manpages.patch new file mode 100644 index 0000000..466996d --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-manpages.patch @@ -0,0 +1,54 @@ +Author: Ole Streicher <[email protected]> +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) diff --git a/sci-astronomy/esomidas/files/esomidas-mdb_put.patch b/sci-astronomy/esomidas/files/esomidas-mdb_put.patch new file mode 100644 index 0000000..eceb4cb --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-mdb_put.patch @@ -0,0 +1,29 @@ +Author: Ole Streicher <[email protected]> +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; diff --git a/sci-astronomy/esomidas/files/esomidas-no-sp_pty.patch b/sci-astronomy/esomidas/files/esomidas-no-sp_pty.patch new file mode 100644 index 0000000..c95893d --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-no-sp_pty.patch @@ -0,0 +1,17 @@ +Author: Ole Streicher <[email protected]> +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\ diff --git a/sci-astronomy/esomidas/files/esomidas-no-strip.patch b/sci-astronomy/esomidas/files/esomidas-no-strip.patch new file mode 100644 index 0000000..5a091ad --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-no-strip.patch @@ -0,0 +1,29 @@ +Author: Ole Streicher <[email protected]> +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 diff --git a/sci-astronomy/esomidas/files/esomidas-propagate-flags.patch b/sci-astronomy/esomidas/files/esomidas-propagate-flags.patch new file mode 100644 index 0000000..3c918e2 --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-propagate-flags.patch @@ -0,0 +1,86 @@ +Author: Ole Streicher <[email protected]> +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 + diff --git a/sci-astronomy/esomidas/files/esomidas-rarthm_for.patch b/sci-astronomy/esomidas/files/esomidas-rarthm_for.patch new file mode 100644 index 0000000..9d4892a --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-rarthm_for.patch @@ -0,0 +1,43 @@ +Author: Ole Streicher <[email protected]> +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 diff --git a/sci-astronomy/esomidas/files/esomidas-selechar_c.patch b/sci-astronomy/esomidas/files/esomidas-selechar_c.patch new file mode 100644 index 0000000..63ff953 --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-selechar_c.patch @@ -0,0 +1,51 @@ +Author: Ole Streicher <[email protected]> +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++) { diff --git a/sci-astronomy/esomidas/files/esomidas-syskeys.patch b/sci-astronomy/esomidas/files/esomidas-syskeys.patch new file mode 100644 index 0000000..96187d5 --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-syskeys.patch @@ -0,0 +1,23 @@ +Author: Ole Streicher <[email protected]> +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 diff --git a/sci-astronomy/esomidas/files/esomidas-system-readline.patch b/sci-astronomy/esomidas/files/esomidas-system-readline.patch new file mode 100644 index 0000000..da06a56 --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-system-readline.patch @@ -0,0 +1,83 @@ +Author: Ole Streicher <[email protected]> +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 diff --git a/sci-astronomy/esomidas/files/esomidas-x11-include-path.patch b/sci-astronomy/esomidas/files/esomidas-x11-include-path.patch new file mode 100644 index 0000000..06aaab9 --- /dev/null +++ b/sci-astronomy/esomidas/files/esomidas-x11-include-path.patch @@ -0,0 +1,13 @@ +Author: Ole Streicher <[email protected]> +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 diff --git a/sci-astronomy/esomidas/metadata.xml b/sci-astronomy/esomidas/metadata.xml new file mode 100644 index 0000000..4055638 --- /dev/null +++ b/sci-astronomy/esomidas/metadata.xml @@ -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>[email protected]</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>
